Here is my personal Update Guide when updating/upgrading Clipbucket.

1. Make a full Backup of all Files and the Database and store it one a different harddrive
2. Never touch a running system! Try to install a new installation first in a different Folder and Database before update the running system.
3. Following Files and Folders should be UNTOUCHED (leave as is) when updating to prevent loss of data.

.htaccess ................................................... (Personal) SEO Rewrite-Rules, PHP-Configuration
favicon.ico ................................................. (Personal) Browser-Favorite-Symbol
/cache ......................................................... Memory for Sessions, Comments and Userfeeds
/files ............................................................ All playable, uploaded Media (Photos and Videos)
/images ....................................................... Avatars, Backgrounds, Category-Pictures, Collections-Pictures, Group-Pictures, Playlist-Pictures
/includes/dbconnect.php ......................... Database-Config with personal Adaption for UTF-8
/includes/langs .......................................... All Language Files incl. Translations
/plugins/cb_server_thumb/cache ........... Cache for Picture Thumbs
/styles/cb_28/theme/images/logo.png .... Personal uploaded Logo in Frontend top left

Instead of overwriting files during update I prefer to delete all files AFTER backuping them, then take the complete folder from update and restore the files and folders listed above. This prevents to have old and unused files left in the installation.

After all I made them all (Files and Folders) recursively readable, writeable and executable (sudo chmod -R 777 /var/www/html/clipbucket/) for Linux Installations.